Sounds like your craft ability fixed the problem, which is always good. When I had my rocker boxes apart, i don't remember noticing any gap in the trough as you describe, and I *think* I would have. I certainly handled them enough for cleaning, and installing the "Cure Vent Plus" kit at the same time. I know I've never had the gasket move totally out of position like yours. When my top plates were warped and leaking, i could move the center ring out of position with my fingers--I knew that couldn't be right.
This vibration thing is downright strange. I wish I had the anser but I'm pretty much stumped. I guess I'd recommend starting over at the simplest and going through all the possibilities as though you hadn't already, and see if you notice something you didn't before.
It'd make me think of heading for the bar, that's for sure.